[rtiangha]

In my experience, the first one is faster (to keep the language clean, I'm assuming you mean Kobo defined Collections, not a bunch of related books all dumped into the same file system folder). I once had a Collection that had over 10,000 books in it (spread out over multiple file system folders because that's how Calibre uploads books; folders based by author) and each tap on anything was slow. Once I deleted that collection, the device was more responsive. Of course, the 2GB database meant things were still slow, but that's a different issue related to lack of RAM.

Another speed tweak you can do is to avoid dumping all your books into one file system folder or into the root directory. FAT32 is inefficient compared to other file systems, so if you have 10,000 books in one file system folder, the OS will have to poll all the items inside each time it has to access the folder (plus I think there's a limit to the number of files that can be in a folder too), made even worse because this is being done on an SD card which is much, much slower than a proper SSD found on a computer. If you're manually copying files over, it's best to separate things a bit into different folders, maybe by author or alphabetically or something.

Finally, if you can, switching to an SD card with fast read speed and fast random write speed can help too; the class of the card is not a guarantee; I've seen Class 6 cards outperform Class 10 cards in terms of random access speed, but you may not have a choice if storage capacity is a higher priority.

And if you're feeling adventurous, you could try switching the user partition from FAT32 to EXT, but you would lose the ability to mount the drive in Windows and Mac without a third-party driver; how to do that is somewhere on these forums.